plier (version 1.42.0)

justPlier: Implements the PLIER algorithm

Description

Provides a wrapper around Affymetrix's API to provide an implementation of the PLIER alogrimth

Usage

justPlier(eset=ReadAffy(),replicate=1:length(eset),get.affinities=FALSE,normalize=FALSE,norm.type="together",augmentation=0.1,defaultaffinity=1.0,defaultconcentration=1.0,attenuation=0.005,seaconvergence=0.000001,seaiteration=3000,gmcutoff=0.15,probepenalty=0.001,concpenalty=0.000001,usemm=TRUE,usemodel=FALSE,fitaffinity=TRUE,plierconvergence=0.000001,plieriteration=3000,dropmax=3.0,lambdalimit=0.01,optimization=0)

Arguments

eset

An AffyBatch object containing the raw data

replicate

A factor containing the replicate structure to use for grouping samples

get.affinities

If TRUE, then return affinities in the description@preprocessing slot of the ExpressionSet object

normalize

If TRUE then apply quantile normalization to the probes before generating expression calls

norm.type

Can be 'separate', 'pmonly', 'mmonly' or 'together'

augmentation

Model parameter

defaultaffinity

Model parameter

defaultconcentration

Model parameter

attenuation

Model parameter

seaconvergence

Model parameter

seaiteration

Model parameter

gmcutoff

Model parameter

probepenalty

Model parameter

concpenalty

Model parameter

usemm

Model parameter

usemodel

Model parameter

fitaffinity

Model parameter

plierconvergence

Model parameter

plieriteration

Model parameter

dropmax

Model parameter

lambdalimit

Model parameter

optimization

Model parameter

Value

An Expression set containing PLIER generated expression calls

Details

This function is a thin wrapper around the Affymetrix implementation. For more details, including information about the meaning of the different model parameters, please see the plier documentation at www.affymetrix.com.

References

bioinf.picr.man.ac.uk www.affymetrix.com

See Also

normalize.AffyBatch.quantiles

Examples